infer_phylogeny: infer the time calibrated phylogeny associated with the...

In thijsjanzen/nodeSub: Simulate DNA Alignments Using Node Substitutions

infer the time calibrated phylogeny associated with the provided alignment. This function uses the R package babette to infer the phylogeny using BEAST2.

Description

infer the time calibrated phylogeny associated with the provided alignment. This function uses the R package babette to infer the phylogeny using BEAST2.

Usage

infer_phylogeny(
  alignment,
  treatment_name,
  tree_prior = beautier::create_bd_tree_prior(),
  clock_prior = beautier::create_strict_clock_model(),
  mcmc_seed = NULL,
  chain_length = 1e+07,
  sample_interval = 5000,
  burnin = 0.1,
  working_dir = NULL,
  sub_rate = 1
)

Arguments

alignment	Phydat object containing the focal alignment
treatment_name	string to be appended to BEAST files
tree_prior	tree prior used, default = birth-death prior
clock_prior	clock prior used, default = strict clock
mcmc_seed	seed of the mcmc chain, default is the system time
chain_length	length of the mcmc chain, default is 1e7.
sample_interval	interval of sampling, default is 5000
burnin	burnin of posterior distribution
working_dir	beast2 working dir
sub_rate	substitution rate used to generate the original alignment (if available), default is 1

Value

list with all trees, and the consensus tree

thijsjanzen/nodeSub documentation built on Nov. 15, 2023, 2:44 p.m.